Cornelius Roemer

Sequences from BY-LGL are all frame shifted due to `-` being `N` in S:69/70del

5

Reviewing latest submissions on GISAID I noticed that a batch of sequences from BY-LGL seems to have a bioinformatics error: Almost all sequences are frame shifted in S1 after S:70...

Very diverse set of sequences with S:P348H (almost exclusive to Germany) in just two submission dates

1

I noticed that there are ~222 sequences from Germany with S:P384H that come from a big range of lineages suggesting the mutation is an artefact. Maybe this is a similar...

Potential sequencing error: S:Q1054E showing up in just Germany on all sorts of lineages

1

Looking at recent German sequences, I noticed that S:Q1054E has suddenly popped up all over the tree - not just in one but in all sorts of lineages. It has...

Germany's RKI publishes received sequences daily to Github and Zenodo. Submissions to GISAID are done only weekly. Hence Github/Zenodo is a few days ahead. I think it would be great...

ENH: Speed up Usher webversion

2

Usher is such an amazing tool. Unfortunately, the run time of analyses using the phyloplace website are quite long. So long that I don't use Usher as much as I...

I've gotten this type of error a few times when uploading my own Fasta file (with maybe some 400 sequences)

ENH: Make `sample type` an Auspice filter

7

I think it would be nice to have `sample type` enabled as an Auspice filter. It should be as easy as adding a few lines to the auspice_config.json that's used...

BUG: Don't get result when uploading about 240 sequences, some of them with spaces in fasta header, e.g. `Czech Republic`

1

When I upload a fasta file with some 240 sequences to Usher through the file picker, I get the following (error?) screen instead of the normal results: I definitely didn't...

BUG: Multiple mutations in one codon cause can cause false amino acid mutation

1

When looking at sequence `Iran/AN127/2022|EPI_ISL_10195257`, I noticed that it was falsely annotated with `Q498*`. Nextclade annotates it with `Q498Q`:  The reason for Usher's false annotation seems to be the...

I wanted to place a potential recombinant fragment that's 9k bp long. Unfortunately, Usher doesn't seem to support this at the moment. Shouldn't Usher still be able to place that...